I don't have Brawl but I'm pretty sure this applies to Brawl as well as it did to Melee. In Melee, eventually I got to the point where everyone I was playing was skillful enough to avoid or block or swipe away the majority of the missiles I shot at them.
Therefore the MAIN use of missiles in my Samus game has been, for a long time now, to bait the enemy into shielding, dodging, retreating, or attacking a missile so I can follow up the lag those things cause and attack them. I don't care too much if super missiles don't KO anymore, I rarely killed with them in Melee and, to be honest, I would be really surprised when one would hit my opponent, as I would be sitting there with the grapple dangling out after trying to grab them (thinking they would shield and NOT get hit)
So missiles are more of a shield than an offensive weapon. whatever distracts and hits the enemy best is what needs to be used, regardless of KO power. homing missiles were too slow in melee. If they're faster in Brawl, they should definitely be used, HugS.